In 1991, he became Education Minister in the first BJP government in the state of Uttar Pradesh. Major highlights of his tenure as Education Minister included Anti-Copying Act, 1992, which made copying a non-bailable offence, rewriting history texts and incorporating vedic mathematics into the syllabus.[4] In April 1994, he was elected into the Rajya Sabha(Upper House of the Parliament) and he became involved with the Advisory committee on Industry (1994–96), Consultative Committee for the Ministry of Agriculture, Business Advisory Committee, House Committee and the Committee on Human Resource Development. On 25 March 1997, he became the President of the BJP's unit in Uttar Pradesh and in 1999 he became the Union Cabinet Minister for Surface Transport.

In 2000, he became Chief Minister of Uttar Pradesh and was twice elected as MLA from Haidergarh in 2001 and 2002.He tried to rationalise the reservation structure in government jobs by introducing the most Backward Classes among the OBC and SC, so that the benefit of reservation can reach the lowest status of Society.

In 2003, Singh was appointed as the Minister of Agriculture and subsequently for Food Processing in the NDA Government led by Atal Bihari Vajpayee, and was faced with the difficult task of maintaining one of the most volatile areas of India's economy. During this period he initiated a few epoch-making projects including the Kisan Call Centre and Farm Income Insurance Scheme.He brought down interest rates on Agriculture loans and also established Farmer Commission and initiated Farms Income Insurance Scheme.

After the BJP lost power in the 2004 general elections, it was forced to sit in the Opposition. After the resignation of prominent figure Lal Krishna Advani, and the murder of strategist Pramod Mahajan, Singh sought to rebuild the party by focusing on the most basic Hindutva ideologies. He announced his position of "no compromise" in relation to the building of a Ram Temple in Ayodhya at any cost and commended the rule of Vajpayee as Prime Minister, pointing towards all the developments the NDA made for the ordinary people of India. He also criticised the role of the English language in India, claiming that it caused erosion of cultural values.

He became the BJP National President on December 31, 2005, a post he held till December 19, 2009. In May 2009, he was elected MP from Ghaziabad in Uttar Pradesh.

On 24 January 2013, following the resignation of Nitin Gadkari due to corruption charges, Singh was re-elected as the BJP's National President.

Singh is on record shortly after the law Section 377 of the Indian Penal Code was re-instated in 2013, claiming that his party is "unambiguously" in favour of the law, also claiming that "We will state (at an all-party meeting if it is called) that we support Section 377 because we believe that homosexuality is an unnatural act and cannot be supported.”

In 2014, Rajnath said that 75 per cent of the people in India either speak or know Hindi.

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